TOMTOM

Name	Alt. Name	Preview	Matches	List
ACAAWRS	2.6e-243	ACAAAGG	8	MA0143.1 (Sox2) , Sox11_primary, MA0442.1 (SOX10) , Sox4_primary, Sox14_secondary, MA0142.1 (Pou5f1) , Sox12_secondary, MA0077.1 (SOX9)
ATTWRCA	3.7e-101	ATTTGCA	3	Pou2f2_3748.1, Pou2f3_3986.2, MA0142.1 (Pou5f1)
CAGCRGG	2.7e-065	CAGCAGG	3	Zic1_secondary, Zic2_secondary, Zic3_secondary
CVATYA	1.4e-064	CCATCA	0
CMCRCCC	2.6e-051	CCCACCC	3	MA0039.2 (Klf4) , Sox13_secondary, Klf7_primary
AYAAWGA	1.2e-047	ACAAAGA	1	MA0442.1 (SOX10)
TRARTR	2.6e-037	TGAATG	0
MGGAAR	7.8e-035	AGGAAG	5	MA0156.1 (FEV) , MA0136.1 (ELF5) , Elf3_primary, MA0144.1 (Stat3) , MA0080.2 (SPI1)
RAGGTCA	3.8e-019	AAGGTCA	10	Rara_primary, Nr2f2_primary, MA0115.1 (NR1H2::RXRA) , MA0141.1 (Esrrb) , MA0160.1 (NR4A2) , MA0065.1 (PPARG::RXRA) , MA0071.1 (RORA_1) , Esrra_primary, MA0065.2 (PPARG::RXRA) , MA0017.1 (NR2F1)
TAATKA	1.2e-017	TAATGA	5	Pou4f3_2791.1, Pou6f1_1731.2, Pou6f1_3733.1, Hoxc9_2367.2, MA0132.1 (Pdx1)
TKTAAA	8.3e-011	TGTAAA	0
GAAARGA	1.0e-009	GAAAAGA	0
ATGCADA	1.1e-009	ATGCAGA	1	MA0142.1 (Pou5f1)
CNCAGC	2.9e-009	CACAGC	2	Zic2_secondary, Zic1_secondary
CCTGBGG	9.0e-008	CCTGGGG	0
GATGGCB	1.7e-006	GATGGCT	0
AAASAAA	3.0e-006	AAAGAAA	0
GGAATGY	5.5e-006	GGAATGT	1	MA0090.1 (TEAD1)
CATTTCC	2.0e-005	CATTTCC	0
CCWCCC	8.6e-005	CCTCCC	0
ASAATAA	1.8e-004	ACAATAA	0
GTCKTTA	3.5e-004	GTCTTTA	0
CTGCRG	5.5e-003	CTGCAG	0

Database	Number of Motifs	Motifs Matched
jaspar_vertebrates.meme	146	18
uniprobe_mouse.meme	386	19

Summary

Alignment

Name	MA0143.1
Alt. Name	Sox2
Database	jaspar_vertebrates.meme
p-value	6.03706e-08
E-value	3.21172e-05
q-value	6.30403e-05
Overlap	7
Offset	8
Orientation	Reverse Complement

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Summary

Alignment

Name	Sox11_primary
Database	uniprobe_mouse.meme
p-value	5.45688e-06
E-value	0.00290306
q-value	0.00217268
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0442.1
Alt. Name	SOX10
Database	jaspar_vertebrates.meme
p-value	6.24201e-06
E-value	0.00332075
q-value	0.00217268
Overlap	6
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Sox4_primary
Database	uniprobe_mouse.meme
p-value	1.00421e-05
E-value	0.00534241
q-value	0.00262155
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	Sox14_secondary
Database	uniprobe_mouse.meme
p-value	2.09082e-05
E-value	0.0111231
q-value	0.00436655
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0142.1
Alt. Name	Pou5f1
Database	jaspar_vertebrates.meme
p-value	5.01902e-05
E-value	0.0267012
q-value	0.00817554
Overlap	6
Offset	9
Orientation	Reverse Complement

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Summary

Alignment

Name	Sox12_secondary
Database	uniprobe_mouse.meme
p-value	6.15524e-05
E-value	0.0327459
q-value	0.00817554
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0077.1
Alt. Name	SOX9
Database	jaspar_vertebrates.meme
p-value	6.26346e-05
E-value	0.0333216
q-value	0.00817554
Overlap	7
Offset	2
Orientation	Normal

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Summary

Alignment

Name	Pou2f2_3748.1
Database	uniprobe_mouse.meme
p-value	5.48103e-06
E-value	0.00291591
q-value	0.00282289
Overlap	7
Offset	4
Orientation	Reverse Complement

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Summary

Alignment

Name	Pou2f3_3986.2
Database	uniprobe_mouse.meme
p-value	5.48103e-06
E-value	0.00291591
q-value	0.00282289
Overlap	7
Offset	4
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0142.1
Alt. Name	Pou5f1
Database	jaspar_vertebrates.meme
p-value	3.48416e-05
E-value	0.0185357
q-value	0.0119629
Overlap	7
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Zic1_secondary
Database	uniprobe_mouse.meme
p-value	1.96726e-06
E-value	0.00104658
q-value	0.00209182
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Zic2_secondary
Database	uniprobe_mouse.meme
p-value	5.83277e-06
E-value	0.00310303
q-value	0.00310104
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Zic3_secondary
Database	uniprobe_mouse.meme
p-value	9.67878e-06
E-value	0.00514911
q-value	0.00343053
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0039.2
Alt. Name	Klf4
Database	jaspar_vertebrates.meme
p-value	6.83696e-08
E-value	3.63726e-05
q-value	7.16678e-05
Overlap	7
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	Sox13_secondary
Database	uniprobe_mouse.meme
p-value	1.14468e-05
E-value	0.00608969
q-value	0.0059995
Overlap	7
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	Klf7_primary
Database	uniprobe_mouse.meme
p-value	4.03691e-05
E-value	0.0214764
q-value	0.0141055
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0442.1
Alt. Name	SOX10
Database	jaspar_vertebrates.meme
p-value	4.73639e-06
E-value	0.00251976
q-value	0.00500296
Overlap	6
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0156.1
Alt. Name	FEV
Database	jaspar_vertebrates.meme
p-value	1.17439e-08
E-value	6.24774e-06
q-value	1.23458e-05
Overlap	6
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0136.1
Alt. Name	ELF5
Database	jaspar_vertebrates.meme
p-value	1.36109e-05
E-value	0.00724101
q-value	0.00715429
Overlap	6
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	Elf3_primary
Database	uniprobe_mouse.meme
p-value	3.24093e-05
E-value	0.0172417
q-value	0.0077747
Overlap	6
Offset	4
Orientation	Normal

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Summary

Alignment

Name	MA0144.1
Alt. Name	Stat3
Database	jaspar_vertebrates.meme
p-value	3.66942e-05
E-value	0.0195213
q-value	0.0077747
Overlap	6
Offset	4
Orientation	Normal

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Summary

Alignment

Name	MA0080.2
Alt. Name	SPI1
Database	jaspar_vertebrates.meme
p-value	3.69781e-05
E-value	0.0196724
q-value	0.0077747
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	Rara_primary
Database	uniprobe_mouse.meme
p-value	3.86847e-07
E-value	0.000205803
q-value	0.000185865
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Nr2f2_primary
Database	uniprobe_mouse.meme
p-value	5.77041e-07
E-value	0.000306986
q-value	0.000185865
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0115.1
Alt. Name	NR1H2::RXRA
Database	jaspar_vertebrates.meme
p-value	6.18258e-07
E-value	0.000328913
q-value	0.000185865
Overlap	7
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0141.1
Alt. Name	Esrrb
Database	jaspar_vertebrates.meme
p-value	8.16049e-07
E-value	0.000434138
q-value	0.000185865
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0160.1
Alt. Name	NR4A2
Database	jaspar_vertebrates.meme
p-value	8.86556e-07
E-value	0.000471648
q-value	0.000185865
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0065.1
Alt. Name	PPARG::RXRA
Database	jaspar_vertebrates.meme
p-value	3.64984e-06
E-value	0.00194171
q-value	0.000637652
Overlap	7
Offset	10
Orientation	Normal

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Summary

Alignment

Name	MA0071.1
Alt. Name	RORA_1
Database	jaspar_vertebrates.meme
p-value	4.97907e-06
E-value	0.00264887
q-value	0.000682562
Overlap	7
Offset	3
Orientation	Normal

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Summary

Alignment

Name	Esrra_primary
Database	uniprobe_mouse.meme
p-value	5.2092e-06
E-value	0.00277129
q-value	0.000682562
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0065.2
Alt. Name	PPARG::RXRA
Database	jaspar_vertebrates.meme
p-value	2.5502e-05
E-value	0.0135671
q-value	0.00297025
Overlap	7
Offset	8
Orientation	Normal

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Summary

Alignment

Name	MA0017.1
Alt. Name	NR2F1
Database	jaspar_vertebrates.meme
p-value	5.42696e-05
E-value	0.0288714
q-value	0.00568876
Overlap	7
Offset	7
Orientation	Reverse Complement

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Summary

Alignment

Name	Pou4f3_2791.1
Database	uniprobe_mouse.meme
p-value	1.0717e-07
E-value	5.70145e-05
q-value	9.29536e-05
Overlap	6
Offset	6
Orientation	Normal

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Summary

Alignment

Name	Pou6f1_1731.2
Database	uniprobe_mouse.meme
p-value	1.02103e-06
E-value	0.000543186
q-value	0.000442792
Overlap	6
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Pou6f1_3733.1
Database	uniprobe_mouse.meme
p-value	6.71707e-06
E-value	0.00357348
q-value	0.00194201
Overlap	6
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Hoxc9_2367.2
Database	uniprobe_mouse.meme
p-value	4.58691e-05
E-value	0.0244024
q-value	0.00994611
Overlap	6
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0132.1
Alt. Name	Pdx1
Database	jaspar_vertebrates.meme
p-value	8.53735e-05
E-value	0.0454187
q-value	0.0148097
Overlap	5
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0142.1
Alt. Name	Pou5f1
Database	jaspar_vertebrates.meme
p-value	1.15677e-05
E-value	0.00615399
q-value	0.0123001
Overlap	7
Offset	7
Orientation	Normal

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Summary

Alignment

Name	Zic2_secondary
Database	uniprobe_mouse.meme
p-value	3.38616e-05
E-value	0.0180144
q-value	0.0211799
Overlap	6
Offset	3
Orientation	Normal

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Summary

Alignment

Name	Zic1_secondary
Database	uniprobe_mouse.meme
p-value	3.9875e-05
E-value	0.0212135
q-value	0.0211799
Overlap	6
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0090.1
Alt. Name	TEAD1
Database	jaspar_vertebrates.meme
p-value	1.26558e-07
E-value	6.73288e-05
q-value	0.000134658
Overlap	7
Offset	4
Orientation	Reverse Complement

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The TOMTOM results consist of

The query motifs with links to further information on matches. [View]
The target databases with information on the number of matches. [View]
The matches between query motifs and target motifs. [View]
- The summary of match information.
- An alignment of the two motifs.
The program details including:
1. The version of TOMTOM and the date it was released. [View]
2. The reference to cite if you use TOMTOM in your research. [View]
3. The command line summary detailing the parameters with which you ran TOMTOM. [View]
This explanation of how to interpret TOMTOM results.

Inputs

The important inputs to TOMTOM.

Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name: The motif name.
Alt. Name: The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website: A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview: The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches: The number of significant matches.
List: Links to the first 20 matches

Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database: The database name.
Number of Motifs: The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched: The number of motifs that had a match with at least one of the query motifs.

Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

Summary Table

The summary gives the important statistics about the motif match.

Name: The name of the matched motif.
Alt. Name: The alternative name of the matched motif.
p-value: The probability that the match occurred by random chance according to the null model.
E-value: The expected number of false positives in the matches up to this point.
q-value: The minimum False Discovery Rate required to include the match.
Overlap: The number of letters that overlaped in the optimal alignment.
Offset: The offset of the query motif to the matched motif in the optimal alignment.
Orientation: The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.

Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type: Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars: Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC: Toggle adding pseudocounts for Small Sample Correction.
Flip: Toggle a full reverse complement of the alignment.
Width: Specify the width of the generated motif.
Height: Specify the height of the generated motif.

Query Motifs

Name

Alt. Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: ACAAWRS (2.6e-243)

Summary

Alignment

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Alignment

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Alignment

Matches to Query: ATTWRCA (3.7e-101)

Summary

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Matches to Query: CAGCRGG (2.7e-065)

Summary

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Alignment

Matches to Query: CVATYA (1.4e-064)

Matches to Query: CMCRCCC (2.6e-051)

Summary

Alignment

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Alignment

Matches to Query: AYAAWGA (1.2e-047)

Summary

Alignment

Matches to Query: TRARTR (2.6e-037)

Matches to Query: MGGAAR (7.8e-035)

Summary

Alignment

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Alignment

Matches to Query: RAGGTCA (3.8e-019)

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